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The gut microbiota

The collection of microorganisms colonising the gastrointestinal tract is called the ‘gut microbiota’.

The human gut microbiota consists of 10-100 trillion symbiotic microorganisms (most of them bacteria, but also archaea, viruses and fungi), with a biomass of over 1 to 2 kg. That means that the number of microorganisms in the gastrointestinal tract is one to ten times greater than the total number of human cells of the human body.
The relationship between humans and their gut microbiota is called a ‘symbiosis’.

A symbiosis between two organisms means that each needs the other to survive. The bacteria in the human body have found a suitable ecosystem for their development; in return these bacteria perform key functions in the body, as described below.

Often misused interchangeably with ‘microbiota’, the ‘microbiome’ actually consists of the collective genetic material of all microorganisms in a specific environment (such as the gut for example). The human genome consists of about 23 000 genes, whereas the gut microbiome encodes around 10 million genes.

Like a fingerprint, the gut microbiota is unique to each individual, and is shaped in early life. Microbiota diversity increases from birth until the age of 3-5 years, when the composition and diversity of the gut microbiota reaches its stable, adult state. In adults, the microbiota is dominated by three bacterial phyla: Firmicutes, Bacteroidetes and Actinobacteria.

The gut microbiota composition is influenced by many factors, of which some can be modified:

Diet and dietary habits (consumption of raw vegetables, consumption of alcohol, consumption of fried foods intermediate fasting, etc.)

  • Weight gain 
  • Medication use (antibiotics, acid suppressants, anti-diabetic drugs, laxatives, antidepressants, etc.) and surgery (colon resection, bariatric surgery, etc.)
  • Breast- or infant formula feeding and introduction of solid food 
  • Environment (rural vs. urban locations) 
  • Lifestyle (exercise, sedentary lifestyle, stress, jetlag)

Other factors are intrinsic, and cannot be changed:

  • Ethnicity
  • Genetic background
  • Certain diseases
  • The anatomy of the intestinal tract (e.g., the large intestine has a higher microbial diversity compared with the small intestine)
  • Gestational age (preterm birth vs. full-term birth)
  • Delivery mode (vaginal delivery vs. C-section)
  • Age and aging
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Although there is a heritable, genetic component to our gut microbiota, environmental factors related to diet, drugs, and anthropometric factors such as weight have a bigger influence on the its composition.
The beneficial effects of the gut microbiota are highly dependent on its composition, which has been shown to change dramatically in several human disorders and diseases.


Humans have a long history of symbiotic interactions with bacteria. Our microbiota has co-evolved with us over thousands of years, to form a complex and mutually beneficial relationship. Indeed, the gut microbiota performs functions that our human cells are not able to.

Key functions of the gut microbiota:


Protection against pathogens by

– inhibiting their growth
– competing with pathogens: the gut microbiota consumes available nutrients and inhabit the available niches, leaving less nutrients and space available for pathogens
– producing bacteriocins, compounds that inhibit the growth of potentially pathogenic microbes

Removal of toxic compounds


Fermentation of food components that are not digested by human enzymes. This fermentation leads to the production of compounds such as short chain fatty acids (SCFAs) These SCFAs are beneficial compounds, as the main source of nutrients of our intestinal cells. SCFA, by interacting with human cell receptors, are also key regulator of human physiology and metabolism
Synthesis of essential vitamins (vitamin K and B)
Modification of bile acids into metabolites able to influence human physiology and metabolism
Increase absorption of dietary minerals (magnesium, calcium and iron)


Strengthening of the intestinal barrier
Training and modulation of the immune system

Bacteria are classified taxonomically according to different groups. From broadest to most specific, these are: phyla, classes, orders, families, genera, species and strains. Only a few phyla are represented in the gut microbiota, accounting for more than 160 species. The dominant gut microbial phyla are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia, with the two first representing 90% of the gut microbiota.

Domain: Animalia
Phylum: Chordata
Class: Mammalia
Order: Primates
Family: Hominidae
Genus: Homo
Species: Homo Sapiens
Strain: Homo Sapiens Sapiens (you)
Domain: Bacteria
Phylum: Verrucomicrobia
Class: Verrucomicrobiae
Order: Verrucomicrobiales
Family: Akkermansiaceae
Genus: Akkermansia
Species: Akkermansia muciniphila
Strain: Akkermansia muciniphila MucT (AktiGut)